


Escape

by flitterflutterfly



Category: Stargate Atlantis
Genre: (Not John or Rodney), Alternate Universe - Canon Divergence, Angst with a Happy Ending, Character Death, Hurt/Comfort, Implied or Off-stage Rape/Non-con, M/M
Language: English
Status: Completed
Published: 2013-02-11
Updated: 2013-02-11
Packaged: 2017-11-29 00:00:06
Rating: Mature
Warnings: Rape/Non-Con
Chapters: 1
Words: 9,684
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/680356
Author URL: https://archiveofourown.org/users/flitterflutterfly/pseuds/flitterflutterfly
Summary: <blockquote class="userstuff">
              <p>When the Genii succeed in taking over Atlantis, John must come to terms not only with his stranded expedition, but also with how his growing feelings for Rodney are suddenly tested to the point of breaking. Meanwhile, the city herself watches in horror at the destruction that approaches.</p>
            </blockquote>





	Escape

**Author's Note:**

> Written for the SGA Reverse Bang. Lovely art (about halfway through the fic) is by Velocitygrass! Thanks to my brother, Egan, for betaing.
> 
> The story is written non-linearally, so don't get confused.

John coughed into the air and then winced as the pain from his constricting stomach set in once more. He knew, intellectually, that he was hungry, but his body was past actually feeling hunger.

He figured he had a couple more days before he died of thirst.

The walls around him moved in, a mirage of exhaustion, but John wouldn’t let himself fall asleep until Rodney was returned to him. Hopefully, by then, he would be able to slip into dreamless sleep, but he doubted it.

At the very least, Rodney’s constant nightmares would wake him up periodically until he got his scientist settled down again.

Not that he’d had much luck helping Rodney. He was useless, stuck in this small room, sitting or standing on the cold floor, just waiting.

Endlessly waiting.

He heard a noise and turned towards the door, but it didn’t open and after a few minutes, John turned back to the bare walls. He’d been trained by the Air Force to entertain himself in hostage situations. It was a common tactic to leave prisoners stewing and by the time they finally came it was almost nice to talk about anything and everything.

But his solitude wasn’t an interrogation tactic. It was neglect.

It was torture.

John took in a deep breath, his lungs on fire in his chest. He ignored that and instead touched the bare grey walls of his holding room, trying once more to feel her.

Atlantis was silent under his fingers.

-._.-._.-._.-

“We have secured the remaining three hunters, Major,” Teyla said through the radio. “Doctor Beckett is bringing the puddlejumper to the gate now.”

“Great,” John replied. “Enjoy Manara, try not to have too much fun without us.”

“I still don’t like it, sir,” Ford stated. “I think I should stay with you and Dr. McKay.”

“Dr. Weir is here also, Lieutenant,” John said. “Think of it as a day off. Dr. Zelenka is sure of this plan and you know McKay, if anything goes wrong he can handle it.”

“I am simply glad that the hunters had already been on their way back to the settlement,” Teyla interjected. “Our people go sometimes on month long hunting trips.”

“They were early?” John shrugged. “That’s lucky.”

“Not early,” Carson said. “One of the poor lads had sprained his ankle a day into their outing and they had to head back.”

“We’ll you’ll get him fixed up, Doc,” John said.

“Do you have everything you need here in case the storm lasts, sir?” Ford asked.

“We’re good,” John told him. “Remember to tell the Manara leader what I said.”

“Will do,” Ford agreed.

Carson coughed. “If you don’t mind, Major, I’m not so sure I can hold the jumper here for too much longer.”

“Go,” John told him. “Try not to hit the gate on your way out.”

“We shall see you tomorrow, John,” Teyla said.

John clicked the radio off and went to go find Elizabeth and Rodney. The door to the control room opened as he neared and John stepped through. “Hey, the last jumper is on its way.”

“Just us now,” Elizabeth smiled. “Good. Okay, Rodney, what do we have to do?”

“Okay,” Rodney flipped his data pad around so they could see. “There are grounding stations here, here, and here…”

-._.-._.-._.-

The door to the room slid open. John was standing even before he could see the people on the other side, but he knew there would be a gun pointed at him.

He was right. The Genii soldier trained the gun to his chest as he threw Rodney back into the room by the arm. John wanted to rush immediately to the scientist, but he knew that if he gave the soldier any excuse at all, the man would shoot, and John couldn’t leave Rodney alone.

The soldier scowled and shifted, the door sliding closed. John stepped towards Rodney the minute he could no longer see the gun. “Hey,” he murmured, wincing internally at how… bland the word seemed. “No luck, huh?”

Rodney didn’t answer. His eyes were unfocused and he shivered, one hand clasping the wound on his arm. John knew he should probably redress it, the Genii had completely mangled the muscles and tendons.

He reached towards the scientist and Rodney flinched back.

John growled low in his throat, burning with the need to take revenge for the man he cared for far too much. He pushed it down, unable to do anything now except comfort Rodney.

“It wasn’t your fault,” he said first, because he’d heard once that was a common delusion by victims of-

“It wasn’t your fault,” he repeated.

Rodney didn’t seem to hear him. John turned on his heels and walked to the corner of the room, punching the wall to let out his rage, but all it did was hurt his fist and give him guilt that he’d punched Atlantis.

Shivering himself, John turned back to Rodney. The scientist hadn’t moved.

“Come on, Rodney,” John cooed softly. “Let’s lie down, go to sleep.”

Rodney didn’t reply, didn’t even show that he’d heard John talk, long enough that John had begun to think he would need to take more drastic measures to snap him out of his shock, but then slowly he nodded and promptly collapsed to the floor where he was.

John lowered himself next to him, far enough away that Rodney wouldn’t feel threatened, but close enough to help if it was needed. “Sleep, Rodney,” he murmured.

He watched silently as Rodney’s breaths evened out and deepened, his face was still screwed up in pain and panic and fear and it had John’s heart racing with too many emotions.

The lights flicked off suddenly and John let out a soft sigh. He didn’t know what this room was originally meant for, but he’d learned that the lights were automatic, turning on and off in perfect sleep intervals.

Still he cursed it, no longer able to see Rodney’s face, to torture himself more with guilt that he could do nothing to ease that pain.

For a long time, John thought about their options and then his mind moved to nightmares before he could stop it. Different ways they all could die. Starving to death as he was… John couldn’t stand it. He wondered if he should give the guard an excuse to shoot him.

He imagined it for a bit, how nice it would be to just go quickly. Just a shot in the chest and it would be all over.

Then Rodney whimpered and he snapped back to reality. He  _couldn’t_ leave Rodney. Not for anything, even the peace of death.

After all, the reason he’d stayed alive for so long… the reason he kept fighting again and again was to atone for the deaths he’d inadvertently and sometimes directly caused.

He knew that if he gave up, so too would Rodney. What was left of that spark in his eyes would leave and John couldn’t do that to the man who yelled and screamed and shouted his arrogance to the world. Rodney was too special.

Without Rodney, Atlantis would fall.

John sighed and turned over, facing in Rodney’s direction. The darkness was an ocean between them, and still he searched as if he’d be able to see the scientist’s curled form.

Eventually, his exhaustion overtook him and John fell into uneasy sleep.

-._.-._.-._.-

“Let me tell you what you did wrong here, Kolya,” John spoke into the radio, adrenaline still rushing through his system and wind rustling his hair into more of a mess than it usually was.

He thought he could hear a gasp come over the radio and he doubted it was the Genii commander. Rodney, he thought.

But he couldn’t think of Rodney then, it would only distract him.

“A), you lost two of your men. B), You damaged the switch before I could separate the grounding rods, which I’m sure you’re gonna get an earful from McKay for,” and that had John thinking of Rodney… He shook himself. “And C), you lost all of what little credibility you had with me.”

He could hear Rodney ranting from the other side of the radio and his lips quirked. They dropped back into a frown as he heard Kolya’s voice come on clearer. “You killed two of my men.”

“I guess we’re even,” John told him.

“I don’t like even,” Kolya hissed back.

John shifted, eyes surveying the two dead men on the ground, then the shot grounding station, and then the storm that was spraying at him. “I’m not finished yet.”

He wouldn’t be. Not until Rodney and Elizabeth were out of Kolya’s grasp and the city was safe.

“Neither am I,” Kolya told him. “Say goodbye to Dr. Weir.”

He wouldn’t. He wouldn’t actually kill Elizabeth, John told himself. But no, he couldn’t be sure of Kolya’s nature, only that he was sounding more and more like men John had run into in the past, men that enjoyed their control over others too much to care about the rules of decent war.

“This city has a self-destruct button. If you hurt her, I’ll activate it. Nobody’ll get Atlantis!” John threatened.

Kolya’s reply was immediate. “Even if it exists, Major, you need at least two senior personnel to activate it… And I’m about to take one of them out of the equation.”

“No!” that was Rodney. There was the sound of cloth rustling and bodies moving and John struggled to picture what was going on. “You can’t do this. This is crazy. You need her.”

“I don’t believe you, Dr. McKay,” Kolya said. “Stand aside.”

“You can’t kill her!” Rodney yelled. “I’m not kidding. There are codes required to activate the shield, codes that only she knows. You can’t do it without her.”

There was a brief pause and then. “Well, you can’t do this without me either. I mean, we’re a package deal. I mean, you take us out of the equation, and you don’t have an end game. Granted, that’s a chess term. My point is, we’re the only ones who can fix the grounding station.”

“I won’t kill you, Dr. McKay. Not yet,” Kolya said. “Stand. Aside.”

“We’re the only ones who can activate the shield. We’re the only ones that can solve problems I can’t even think of yet. You kill either one of us, and you don’t get what you want! That’s how important we are. It’s impor-”

Rodney’s voice was breaking, as if he was about to cry, and John swallowed hard because he already knew what the end game was.

_No._

“Hold onto him,” Kolya snapped.

“Kolya? Kolya! I’ll give you a ship! I’ll fly it out of here for you myself!” John pleaded as he heard Rodney yelling in the background. “Kolya!”

Then the all-too familiar sound of a gunshot cracked through the water-ridden air and John closed his eyes.

“ELIZABETH!” Rodney screamed.

“I’m going to kill you,” John promised, the cool calm that he’d come to associated with his most dangerous rage spreading through him like a storm of its own.

-._.-._.-._.-

John woke like the snap of a rubber band, one minute asleep and the next fully alert. He kept his eyes closed and his breathing even, using his other senses to figure out what had woken him.

There was a soft sound, almost a whimper, and John relaxed just slightly. He turned over onto his side, eyes blindly pointing in Rodney’s direction. “Rodney,” he whispered.

Rodney’s cries became more muffled, as if he’d curled up on himself to escape the humiliation of John seeing him. The first couple of nights, John had let him, but he couldn’t do that anymore.

He couldn’t stand to see Rodney suffering.

John scooted on the cold metal floor. “Face me, Rodney. Look at me, please.”

He could see the outline of Rodney’s body in the dark as Rodney shook his head. John sighed. “I’m going to touch you, okay, don’t be afraid.” He reached forward slowly and grasped Rodney by the shoulder.

Rodney’s muscles flinched under his arm and his whole body froze. John took a chance and pulled Rodney around so that they were facing each other. He reached a hand for Rodney’s face and pulled his arm away from it.

“John,” Rodney said brokenly.

“I’m here,” John reassured him. “Come here, it’s me.”

Rodney didn’t move, so John moved for them, wrapping his arms around Rodney loosely and holding him. After a moment, the scientist unfroze and began to shiver again, and then his head came to rest in the crook of John’s neck and John felt wet tears begin to drip down his shoulder.

His hatred for Kolya grew again, surpassing even his own expectations made in the hour after Elizabeth had been killed. It still hurt, thinking about her, and he supposed that might never stop hurting. She’d been one of the best commanders he’d ever had, and one of the few he could call friend.

But all the events that had followed Elizabeth’s death had begun to overshadow that catalyst event and now his rage was fueled not by her untimely demise, but by the physical and emotional pain Kolya had caused and continued to cause Rodney.

Everything came back to Rodney.

“You must think I’m really pathetic,” Rodney said, his voice muffled by John’s body.

“No,” John told him, squeezing his arms as tightly as he dared. “Never. This isn’t pathetic.” His throat dried and his next words came out so softly that he wasn’t even sure Rodney could hear him, but he had to try. “Kolya’s the pathetic one. He has to take what he would never be able to get and he’ll never understand what it’s supposed to mean.”

“Atlantis is too beautiful to stay under his control,” Rodney’s head pressed closer to John’s neck and John responded by shifting closer to Rodney’s body.

And though he hadn’t been talking about Atlantis, or at least not just about her, he couldn’t say that. He’d always had a hard time talking about his feelings, even in normal circumstances. The circumstance they were in was anything but normal.

“I should…” Rodney began, pulling away.

“No, please,” John begged, tightening his arms. “Let me take care of you, like this.” His pressed his nose to Rodney’s blood-matted hair and closed his eyes. “Please, Rodney.”

Rodney’s response was slow coming, but eventually he nodded and John relaxed. He wanted to say so much, then. He wanted to show Rodney, to prove to him that he didn’t think him weak or pathetic or deserving at all of what Kolya did again and again. He wanted to tell him that he loved him.

By the time he opened his mouth to say anything, Rodney had relaxed back into sleep and John couldn’t let himself wake him.

At least, with Rodney in his arms, he felt stronger than he had since he’d first been put in this damn room.

-._.-._.-._.-

“Major Sheppard,” Kolya said. “I have a proposition for you.”

John’s vision black out for a brief second and then he contained himself. “Kolya I’m having a hard time keeping up. What’s the score again?”

“My men have informed me that not only have you disabled some crucial generators, but you’ve stolen key components which make it impossible for them to be restored,” Kolya stated.

“Yeah, I did that.”

“There are two flaws in your plan.”

“I’m always open to constructive criticism.”

“One, the assumption I would believe you’d rather destroy the city than let it fall to us is childish.”

“Doesn’t sound like me.”

“Second, if and when I determine Atlantis unsalvageable, Dr. McKay becomes obsolete.”

John stopped short. He wanted to argue, to tell himself that Kolya wouldn’t do that.

He’d already done that once and now Elizabeth was dead.

“What do you want?” he heard himself asking.

“We have less than one hour before the storm hits full-force. If the power is not returned to grounding station three within the next ten minutes, Dr. McKay dies,” Kolya said. “We will then leave with what we can, and the city will be destroyed.”

“Well, that’s not enough time!” John protested immediately.

He could practically hear Kolya’s smirk as he said his final offer. “If you don’t mind destroying Atlantis, stay where you are for the next ten minutes…starting now.”

John didn’t know where his speed came from, but he made it to the generator and activated it within the first few minutes, his mental dialogue deadly silent as he ducked around the doorway and escaped from the room they would all now know he’d just been in.

He was only two hallways away from the control chair, and that was where he went next. The door slid open for him as if it had been waiting and he stepped inside. He knew too well that now that the power was back on, it wouldn’t be too long before Rodney finished fixing the power station and then Kolya would make him activate the shield around the city and then he’d be obsolete.

They’d both be, but John had never cared much for his own life except in the way that if he died, he wouldn’t be able to protect Rodney.

The possibility of Rodney dying burned like the Afghani sun on his back, unceasingly painful. He thought perhaps that, were Rodney to die, he too would lose the only part of himself he liked anymore.

How many months had it been since they’d come to this fine city? Since he’d met Dr. Rodney McKay? Since he’d learned to like that part of himself again?

John sat down on the control chair and closed his eyes as it turned and leaned back. Immediately, it was as if his mind was being flooded with sensory information – anticipation and fear of the storm to come, anger at the invaders, and a brush of sadness for those who’d died before it faded.

“Atlantis,” he murmured in sudden realization. He’d felt her before, but faintly and never like that had just been.

There was a tug and John tried to follow it, only to lose the connection a moment later. The tug came back. He grabbed onto it, trying to tether it to himself as it got weaker and weaker.

“Come on,” John said.

There was a blast of light behind his eyes, as if he’d found the light at the end of the tunnel, and then he could  _feel_  her inside him.

She murmured sweet nothings, sparks of emotion and blasts onto his senses before fading again. He tried to ask her what was wrong, but all was silent. And yet, it was as if she’d heard him anyways as she pulled him to her core.

Three power sources lit up like stars, before flashing to show the reality. One, almost depleted ZPM.

He tried to apologize, to say they were trying, and she soothed him. It was her turn to ask  _him_  what was wrong.

John’s mind flashed to Rodney’s bright blue eyes and his crooked smile, then Kolya’s voice drifted in his ear and the city shook with anger.

She told him that she would help however she could. That she trusted him to find her more power. That they would rescue her other leader.

 _Leader?_  John asked.

She answered that only with a hint of contentment that quickly disappeared.

 _How do I save you?_  John asked then.  _You and Rodney._

The image of the gate flashed in his mind, and then Ladon cheering as he overrode John’s protocols. Atlantis seethed in his mind.

 _Close it_ , he told her.  _Close the gate. Keep it closed. Can you do that?_

 _Of course_ , she seemed to say and then the image of Ladon scowling flashed as he tried to activate the gate only for it to fail.

John grinned.  _Great, keep it closed, no matter what happens._

Atlantis touched his mind, as if she wanted to say that would be all she could do. She feared for him, him and Rodney.

He reached for her, accepting and understanding her worries, and then let her go.

The chair turned back and sat up and John opened his eyes to an empty room. He checked the radio and winced, wondering how much time had passed. Clutching his suddenly pounding head, John staggered out of the control room and back in the direction of the main command center.

He was just turning the corner around the generator station he’d recently repaired when he found himself facing two guns.

“Shit,” John cursed. He should have gone a different way, but it was too late to change that now. He put up his hands, taking them off his P-90.

One of the guards spoke into his radio, “Sora, we have him.”

“Good,” Sora said through the radio. “Bring him to the gateroom. The commander has told us to fall back to the central tower.”

The guard nodded, though Sora wouldn’t be able to see. “Understood.”

John closed his eyes, hoping Atlantis would hold the gate, and let them take his vest away.

At least, he thought, he’d get to see Rodney one last time before he was killed. After all, there would be no reason to keep him alive, not when he’d already killed over seventy of Kolya’s men.

-._.-._.-._.-

John woke to Rodney shifting in his arms. “Morning,” he said.

Rodney sighed and moved away. John reluctantly opened his arms to let him go. “Hi.”

Sitting up, John surveyed Rodney’s blotched face. There were dark bags under his eyes and a large wound on his forehead that had scabbed over by now. It still had John’s heart clenching in his chest and he moved his eyes to Rodney’s own.

Rodney watched him silently, his gaze sharper now than it had been last night. “You’re sick.”

“I’m starving,” John argued. “Not sick.”

Rodney winced and nodded. John knew that he’d been getting food, that Kolya used food as a reward when he didn’t struggle. He didn’t blame Rodney for it, but he knew Rodney would continue to feel guilty.

“You know, I’m bisexual,” Rodney said suddenly. “I probably shouldn’t tell you that-”

“You don’t have to hide anything from me,” John interjected before Rodney could finish his statement. “I’m,” he took a steadying breath, “I’m gay.” It was hard for him to say, the last time he’d told someone he’d gotten kicked out of his own house and then he’d joined the Air Force and that was that.

But Rodney was smiling softly at him. “I didn’t know.”

John nodded. “Not many people do.”

Rodney turned his face away. “I never thought sex could be painful, you know? I just… I mean it’s been awhile so I knew it’d be a bit hard on me, the next time… but when he… it  _hurt_.”

John reached forward and touched Rodney’s arm lightly. He didn’t know what he could do to comfort his blue-eyed scientist, only that he had to do something.

“We can’t go on like this,” John murmured.

Rodney chuckled bitterly. “What choice do we have?” He paused. “Other than death.”

John winced. A couple more days and he’d be too weak to stand, let alone save them both. Even now, Rodney was the stronger of the two of them, at least physically. John knew they’d have him die of thirst before they did anything about his growling stomach.

And once he was dead, how long would it take before Atlantis to lose her power completely. The failsafes would reactivate the gate at least enough for one more wormhole and then the Genii would escape unscathed.

“We have to try,” John said. “We must.”

Rodney’s eyes burned into him, but John couldn’t explain himself then.

“Okay,” Rodney said. “What do we do?”

John took a deep breath. He wasn’t sure what they  _could_  do. “Let’s talk it out. How many men does Kolya have left?”

“Five, I believe,” Rodney frowned. “Along with Sora and Laden.”

“And Kolya,” John said. “So that’s eight.” Not too many, and usually he’d be fine with those odds, but he was weak and they were stuck in a room until the next time a man came to bring Rodney to the Genii commander.

An idea donned suddenly and John jerked up straight. “How about we do this?”

Rodney listened as he explained, his face growing white but his eyes determined.

“Can you do it?” John asked as he finished. It would put even more upon Rodney’s shoulders.

“It’s the only plan that could possibly succeed,” Rodney said. He closed his eyes and nodded. “I can do it.”

 

-._.-._.-._.-

The guard prodded him forward with a gun to his back. John was only glad he didn’t stumble and destroy his calm image as he was pushed into the command center.

Rodney stood next to Kolya, his shoulders hunched miserably over the laptop. He looked up as soon as John neared, a flash of stark relief coming over his face. “You made it.”

John nodded, but didn’t speak as he turned his eyes to the man he assumed was Commander Kolya of the Genii.

Kolya’s dark eyes met his squarely, and then turned on Rodney. “The shield, Dr. McKay.”

Rodney hesitated, his fingers still on the keys as he glanced again towards John. John nodded brusquely. “Save our city, Rodney,” he murmured. He supposed that they could have tried to fake it, maybe say the shield wasn’t working, but with Atlantis blocking the gate there would be no where for them to go.

Kolya’s face morphed into anger, almost possessive in nature as he looked at John. John raised an eyebrow, but inside he grew cold at what that meant.

Rodney wasn’t Kolya’s.

Bolstered, Rodney quickly typed in the code. “And, there.”

“A massive wave is approaching from the West,” Ladon said from the other monitor. “Without the shield-”

“It’s working. It just needs to build up enough power for the shield to activate. Wait for it,” Rodney’s eyes flashed across the screen in front of him. “Lightning is hitting the conduits. Last chance to get out of the halls… and… here we go.”

The city shuddered around them. John caught himself on Rodney’s shoulder and Rodney leaned into him. “Is it working?” Sora asked over the sudden clatter of noise.

“It’s working!” Rodney told her over John’s shoulder.

“The shield has engaged around the city,” Ladon told them all. “The wave has passed.”

John’s shoulders relaxed slightly and his arm curled protectively around Rodney. He felt a prickle on his neck and twisted his head to see Kolya watching them.

John stiffened, but too late. He knew what Kolya had seen and what he would take from that scene. There was no doubt he would use that against them both. Or at least, against John. He had no doubt that Rodney was just comforted by a familiar presence, the fact that it was  _him_  was inconsequential.

But maybe that’d make it easier on the scientist. He hoped so, no matter how much he wished for Rodney to return his feelings.

“Commander,” one of the guards said. “I have found a room as you asked.”

“Good,” Kolya nodded. “Put them in it and return here. Ladon, I want you to get started on fixing the ring of the ancestors.”

“Yes, sir,” the guard and Laden both said and then John and Rodney were being prodded by gunpoint out of the control room and towards one of the yet-explored rooms of the central tower.

The door opened as the guard put his hand on the side switch and he gestured with his gun for them both to step in.

They did and the door was closed behind them. John looked around the empty room and a sense of dread overcame him like the last of the tidal surge.

They was no more reason to keep either of them alive now, was there?

-._.-._.-._.-

Though he’d spent who knows how long in the room that had become his cell, the last few hours after they’d made their plan and before the guard came to get Rodney were worse than any except the first day.

The first day had been…  _bad._

“Why Air Force?” Rodney asked suddenly.

John blinked and looked over at him. “Huh?”

Rodney rolled his eyes. “Air Force. Why? Why not Navy. I’m mean, I’m assuming you wanted to fly… Navy has the better helicopter units, right?”

John frowned. “My dad was Navy, before he went into business.”

“Business?” Rodney asked. “Wait, Sheppard Industries? Is that yours?”

“It’s my dad’s,” John nodded. “Not mine.” It would never be his, his dad had made that clear, but John didn’t care much. He never wanted to be grounded and running a multi-million dollar corporation would ground him totally.

“Huh,” Rodney’s mouth turned down in that crooked half-frown of his, the one that said he was contemplating something.

In Rodney’s right hand was a knife. John had been relieved when the Genii hadn’t checked his body for anymore weapons after they’d taken his P-90 and handgun, but he’d learned quickly that any move in the direction of the guards had their trigger fingers tightening and so he’d kept his distance, never able to use his backup weapon.

Now, it would be Rodney’s duty to go for the kill so they could escape.

“You have any other family?” Rodney asked.

He was trying to distract himself, John realized, so he answered. “Just a brother. Older by a couple years. He has a wife and kids, but I don’t see them often.” Or ever, he thought.

“I have a sister,” Rodney said. “I haven’t talked to her in… two years. We had a fight, last year.” He was looked at his lap, his fingers playing with the knife. “She had a kid and dropped out of grad school and I told she was ruining her life and now… now I’m on Atlantis.”

“I’m sure you’ll see her again, Rodney,” John said.

“If we ever reconnect with Earth,” Rodney took a deep breath. “If we ever do then I’m going to go visit her. I’m going to apologize for shutting her out of my life. I don’t even know the name of my niece, you know. That’s… I don’t remember where my priorities had been, but one thing the Pegasus Galaxy teaches you is how to re-prioritize, right?”

“She’ll forgive you,” John told him. “She has to.”

Rodney huffed. “My sister is about a stubborn as me. If I told her that…”

John shifted and put a hand on Rodney’s knee. “If she doesn’t, I’ll go to her house and make her myself.”

Rodney laughed, which was good, and then he sobered a little. “I’d like you to come with me,” he said finally. “Emotional support.”

John’s throat constricted. “I’d like that.”

Then the door opened suddenly and they both froze, before scrambling to their feet.

The guard kept his gun pointed at John, like he always did. It was funny, in some ways, that all of the Genii considered John more of a threat than Rodney. Hell, most of John’s soldiers would say the same.

Ask any of the scientists, though… John could kill a person with his bare hands. Rodney could blow up a planet. That was the difference in their power, and John knew it.

In this instance, though, the Genii’s underestimation of Rodney’s abilities was to their advantage.

Then again, the soldier had probably been witness to Rodney at his utter weakest. Humiliated, defeated, in pain.

John glared at the man and the soldier shifted uneasily. “Let’s go,” he said to Rodney, his eyes not even moving away from John’s face.

Rodney stepped forward, walking up the guard with one hand behind his back. John continued to keep his eyes on the solider so as not to give the plan away, not to get Rodney hurt.

Rodney moved quickly, the knife jutting out of the guard’s chest before the man could even pull the trigger on John. John ducked the side, just in case the man did shoot in the last few minutes of his life, but by the time he’d looked up again, the guard was dead on the ground.

Standing over him, Rodney shook slightly. His throat moved as he swallowed hard and he’d grown even paler. John walked up to him and wrapped a hesitant arm around his shoulder.

“You okay?” he asked softly.

Rodney shook under his arm. “That’s the first time I’ve killed someone up close before,” he admitted. “Sorry, just… give me a minute.”

John did, even though they need to move before Kolya got impatient and sent more guards. But every soldier went through this phase after they killed their first man.

In every soldier’s file was that exact moment when they turned from civilians to killers. John hoped that Rodney would never become okay with death, not like John had so many years before.

“We need to go,” John said finally.

“Yeah, okay,” Rodney nodded. He stepped through the door, turning to look at both ends of the hall as John retrieved both knife and gun from the guard’s body.

-._.-._.-._.-

“What is this room?” Rodney asked to himself, pacing towards the door again. “There’s no inside control panel at all!”

“Maybe it was the time-out spot,” John suggested dryly.

“For naughty Ancient children?” Rodney snorted. “Yeah, right.”

John shrugged, but inside he was fretting just as much as Rodney. “There’s nothing you can do, Rodney. Sit down, we need to conserve our strength.”

“Hmph,” Rodney shook his head, but he sat regardless. There was silence for several moments, then Rodney sighed. “I’m hungry.”

John winced. “I could use some water.”

“I’m hypoglycemic, you know,” Rodney said as if John hadn’t spoken. “I need to eat soon, or I’ll die.”

John wanted to mention that they’ll probably die anyway, but he knew that Rodney knew that. Knew that Rodney was just trying to distract himself.

It was one of the things he’d figured out about the scientist. Half the insincere or stupid things he said were because of his anxiety. It should turn John off, someone so arrogant and insecure, but instead it made him even more interested in Rodney.

“John,” Rodney murmured.

John looked over, wondering when they’d started calling each other by their first names. “Yeah?”

Rodney was looking straight ahead, his shoulders tense and his hands clenched together. “I got Elizabeth killed.”

A harsh intake of breath, and then John was shaking his head harshly. “No, no Rodney. That was not your fault. They… Elizabeth knew the risks when she stepped through the gate, okay?”

“He just shot her,” Rodney stated quickly. “I couldn’t do anything.”

“You tried,” John reminded him. “Rodney, look at me.” He waited until Rodney did and caught him with an honest glare. “Don’t blame yourself. Don’t go down that road. Elizabeth wouldn’t want that, you know she wouldn’t.”

It was something that had to be told to him. Something he still wasn’t good at reminding himself. An image of Holland flashed through his mind and he turned away from Rodney’s suddenly sharp eyes.

“How many people have you lost before?” Rodney asked.

John let out a harsh breath. “Too many,” he admitted.

“One is too many,” Rodney countered.

John bowed his head. “True.” He took a shuddering breath, Elizabeth’s determined gaze, her relieved smile, her sharp words and kind heart… all of that consumed him.

He forced it to simmer down, to be contained in that cage inside his mind where he kept Holland and Dex and Mitch and his mother all the others he’d lost over his life.

He hoped he wouldn’t have to push Rodney in that cage. He didn’t think he’d be able to. No, he knew he wouldn’t.

Rodney meant too much, was too large a person to ever fit in that cramped cage.

“How are we going to tell the expedition?” Rodney asked. “We don’t have a leader anymore.”

“We do,” John said. “Us, the two of us. We can lead this expedition. We’ll have to.”

Rodney frowned. “Grodin and Zelenka can take over more of the scientific responsibilities,” he acknowledged finally. “Just until we reconnect with Earth, right?”

“We’ll find a ZPM,” John told him. “I promised At-” he cut himself off as the door opened.

Kolya stood on the other side, a guard at his side pointing his gun at John. “Stay where you are, Major,” the commander said as John made to stand up. “I have a question for Dr. McKay.”

John and Rodney exchanged a quick glance.

“The ring of the ancestors,” Kolya stated. “Or, what do you call it?, ah, yes, the stargate. Despite Laden’s best efforts, it is failing to engage.”

“Might be interference from the storm,” John said, shrugging.

“I did not ask you, Major,” Kolya scowled. “I asked Dr. McKay.”

John glared as Rodney shook his head. “I can’t know unless I see it,” he stated. “But Jo- the major might be right.”

“The storm has passed.” Kolya raised an eyebrow.

Two heartbeats and no one spoke. Finally, Kolya sighed. “Very well, Dr. McKay, come with me. Major, you can stay here.”

John stood, ready to fight his way out instead of letting Kolya take Rodney, but Rodney laid a hand on his arm and shook his head. John opened his mouth to argue, only Rodney had already made his way to the door.

As soon as he was in Kolya’s grasp, he was grabbed by his arm and twisted into Kolya’s chest. “Let’s go,” Kolya said with a nasty grin.

John vibrated with fury as the door closed behind them. He glared at it for several minutes, as if he could open it with his mind. He could, sometimes, and he now knew that was probably Atlantis. Except he wasn’t sure the extent of her reach.

He could try. Walking to the door, John put a hand on it and closed his eyes. He took a deep breath and pushed out with his mind, trying to find that connection he’d had on the chair.

There was the faintest brush against him and then it was gone. John tried again, pushing as hard as he could, but the room was silent around him and the door remained closed under his hand.

John leaned his head against it, his eyes still closed as he waited.

Hours later, when it opened again, John had retreated back to the corner. Rodney was unceremoniously dumped onto the floor and the door was closed just as quickly as it had been opened.

“Rodney!” John called, rushing over to his teammate. He turned him over and found the scientist’s eyes unfocused. “Rodney, are you okay?”

“I couldn’t figure out,” Rodney croaked. “The gate- the gate wouldn’t work. They, he, I couldn’t- I wasn’t lying.”

John opened his mouth to tell Rodney about Atlantis, to say that he couldn’t have figured it out because Atlantis was working against him to save them.

But Rodney had turned over, shivering, and John saw the blood seeping through his jacket arm and he swallowed hard. “You’re hurt,” he stated. “Rodney, Rodney stay with me.”

Rodney groaned and John felt his heart constrict in his chest.

-._.-._.-._.-

The hallways were empty as they raced down them. John thought he could feel the remaining traces of the electrical storm that had powered the city enough to create the shield, but it could just have been his imagination.

“Hold,” John said. Rodney stopped immediately and John peered around the corner, his gun leading his sight, before he nodded Rodney ahead. Rodney quickly stepped into the transporter and John followed.

Rodney pressed a button on the back screen and John raised his gun again, though he doubted any of the Genii would be near Rodney’s lab.

They weren’t. Rodney quickly entered his command code and stepped inside. John left him there and headed to the nearest weapons storage, where he traded his Genii gun for a P-90 and several extra ammo clips. He strapped on a bulletproof vest and grabbed another one for Rodney.

After a moment, he frowned and grabbed a pistol for Rodney too. They’d been working on his aim and though Rodney still had quite a ways to go, he was proficient enough.

John jogged back to the lab in time to see Rodney unplugging a laptop. “Ready?” he asked.

“Yeah,” Rodney nodded. “I need to tap into the circuit line of the command tower. Let’s go.”

“Here,” John said, handing the vest and then the gun over. Rodney frowned, but accepted both. John grabbed the computer so Rodney could slip on the vest and then stick the handgun in it.

A minute later, and they were racing back down the hallway again, though this time back in the direction of the command tower. John kept his eyes and ears open, aware that they could run into a Genii at any minute.

“Here,” Rodney said, stopping. He reached for a panel on the wall and pull out a cord, plugging it into his laptop. Balancing the computer on his forearm, he began to type with one hand.

John heard footsteps coming down the hallway and he slid up against the wall, gun ready. The soldier came around the corner, gun already raised, but John was faster as he pulled the trigger of his P-90.

The Genii fell backwards, mouth open in shock. His body hit the ground with a thud and a shudder, before he fell still and dead.

John’s mouth twisted grimly, but when no more guards came after several minutes, he walked back over to where Rodney was watching him. “You go it?”

“Yeah, just give me a second,” Rodney murmured, his eyes moving back to the screen. He hits three keys in rapid succession, making a small noise of success as the laptop flashed to show a video feed from the command room.

John frowned the minute his eyes laid upon Kolya and he could feel Rodney grow stiff besides him. There was only five in the room, just Kolya, Sora, Laden, and two guards. Which mean there was one more out in the corridors, assuming their count was correct.

“Can you lock them in?” John asked.

“Done,” Rodney answered immediately, typing in a quick code with his open hand. “I’ll override it when we get to the door.”

“Good,” John nodded. He watched as Kolya said something to Laden, his posture angry. Laden flinched back and Sora paled. John was only glad that Kolya’s own men were just as scared of the monster as they should be.

“What did you do?” Rodney asked suddenly.

“When?” John tilted his head to the side and glanced at Rodney out of the corner of his eyes.

Rodney turned to face him. “To the gate. What did you do to it?”

John inhaled deeply. “Oh.”

“I know you did something,” Rodney said. “I just can’t figure it out. It wasn’t anything I could override, which is a good thing I suppose, because Laden will never figure it out, but…”

“It was to protect you,” John said, and then amended quickly. “To protect the city.”

But still, he was glad Rodney was still as sharp as ever. His eyes were clear and John attributed that to the fact that they had an escape plan. That they could get out of this alive and, if not whole, at least they could recover.

How could Rodney ever think himself weak? John asked himself as Rodney continued to stare at him. Stronger men than Rodney had fallen apart over what Kolya did to him, and yet he was still so determined to survive. To continue to live his life.

He was so strong. So very strong and beautiful.

John opened his mouth. “I love you.”

Rodney’s eyes widened. It would be comical except that John’s heart was pounding in his ears.

“John,” Rodney murmured.

John smiled softly. “Sorry, I know it’s not the best time, but…”

Rodney shook his head and then slowly, hesitantly, leaned forward. John met him halfway there, their lips touching like a power surge. John groaned into it and pushed closer, only to have Rodney retreating.

“Sorry, sorry,” John said immediately, getting out of Rodney’s space. “That was-”

“Don’t,” Rodney cut him off. “It’s okay. He… you’re not him and he never kissed me anyways.” Rodney grimaced. “I’m sorry I’m so…”

“You’re not,” John reassured him. “God, Rodney you’re perfect. You’re so strong and beautiful.” It was a relief to finally say the things that had been on his mind and he let that show in his eyes.

Rodney softened and leaned forward again, giving John another kiss. John let him take control of it this time, though he wanted nothing more than to wrap Rodney in his arms and hold him tight.

Now was not the time.

John pulled back this time. “We don’t really have time for this,” he murmured.

Rodney nodded and licked his lips. “Right.” He closed his laptop and unplugged it, sticking it under his arm.

John pulled back the urge to kiss him again and instead he began to explain. “Atlantis is sentient. Or, at least, she’s has an extensive AI.”

“Okay, what?” Rodney frowned.

“I’ve felt her before,” John said. “But I thought it was my imagination. You know how the Ancient technology seems to sort… read your mind? Well, I think that’s her. Or part of her.”

“It- she was designed to discover the needs of the user and cater to them,” Rodney nodded slowly. “Okay. So the gate…”

“I went to the chair and I connected with her,” John explained. “She needs power, Rodney. She’s so weak.”

Rodney’s eyes flashed with determination. “Of course. As soon as we regain our city, save Atlantis, we’ll get her a ZedPM.”

John smiled. “She’s blocking gate travel so the Genii can’t come or go until we say.”

“I see,” Rodney murmured. “Okay, then.” He took a deep breath. “Onto phase two?”

John nodded. He led the way down the hall, stepping over the dead Genii as they made their way to where Kolya and his men were locked inside the command tower.

John pushed down his panic. “Focus, Rodney, focus on me.”

Rodney’s gaze flickered and it gave John hope that he was listening. “I’m going to take your jacket off, okay?”

No response, but John pushed past it, sitting Rodney up and tugging the jacket first from his unhurt arm and then past the hurt one. Rodney cried out as the cloth peeled away from the bleeding wound and John winced. “Sorry, sorry,” he murmured as he set the jacket aside.

The wound was deep, extremely deep. John could see the hint of the bone at the bottom and his own arm ached in sympathy. It needed stiches at the very least, but he didn’t have anything he could use so instead he settled for ripping apart Rodney’s jacket into large strips.

“Lemon,” Rodney muttered.

“What?” John asked as he tightly wrapped the arm.

“Don’t put lemon,” Rodney said, his eyes still dulled.

John bit back a growl. Rodney was allergic to citrus, he remembered, and he hoped that it was only when orally ingested. Regardless, putting lemon on a cut that deep… no wonder Rodney had told Kolya the plan earlier.

“There you go,” John said. He frowned, noticing Rodney’s strange angle. “I’m gonna shift you.”

Rodney coughed, once, and John grabbed him by his shoulders, sitting him up more and moving him onto his ass.

Rodney cried out in pain and John froze. “Rodney?”

The scientist shivered, twisting out of John’s grasp. “No, please, no more. I don’t know, I don’t know anything. I promise.”

John took a shuddering breath and moved a hand to Rodney’s back and then down.

“No!” Rodney jerked and then grew still and silent.

John wrenched himself away, scrambling back so that he was no longer touching Rodney. He knew what was happening, Rodney had escaped into himself. An escape from the pain that had been inflicted upon him.

John wondered if the wound on his arm was just secondary to him now. It was still certainly the most dangerous physically. Psychologically, though.

The idea that Rodney would be altered by this was terrifying, but John’s terror soon caved way to cold rage as the full realization of Rodney’s situation was. He wondered if it was just one or if more had joined in.

“Fuck,” John cursed and then banged his face into his hands as the word just produced more nightmarish images to plague him.

Once, when he was a teenager, he and his dad had been watching the news and there was a story about a serial murder who went to gay bars and found victims to violate and then kill.

His dad had sneered at the TV. “Serves them right,” he’d said. “Faggots.”

John had been silent, because by that point he’d already had his first kiss and it wasn’t Suzie next door, but Gary down the street.

Sometimes, John wondered if he would never have married Nancy if he hadn’t gone Air Force. Or if his father hadn’t kicked him out of the house. It was a combination of the two, he thought, that had him finding a woman whom he’d liked, for her personality if not for her gender.

It certainly had gotten a number of his commanding officers off his back and they’d gone back to overlooking his occasional longing stare. It hadn’t however, gotten his dad talking with him again and the man hadn’t even come to the wedding.

The divorce, a year or so later, had been a relief.

Right now though, his dad didn’t matter. Hell, even the Air Force didn’t matter. They were stuck in another galaxy with no contact with Earth. Who the fuck cared if John was gay and in love with his CSO?

He was in love with Rodney.

John looked over in Rodney’s direction only to find him curled up in the fetal position. He winced and looked away, knowing that if he looked over again he would have to do _something_  and something would not be a good thing. Not in this situation.

John closed his eyes and pressed his face against the wall, angry and feeling more useless than he had since his mom passed away.

Nothing mattered anymore except getting Rodney out of Kolya’s grasp. He wanted to rip Kolya apart, to tear him away until he could never even  _touch_  Rodney again.

-._.-._.-._.-

They ran into the last guard as they were rounding the final corner before the main door to the gateroom. Surprisingly, it was Rodney that shot first, though he hit the guard in the leg. Still, it was enough to give John the second’s advantage it took him to round off into the man’s chest.

“Just those in the command tower left,” Rodney said.

John nodded. He approached the door and listened inside. All he could hear was muffled voices, though, so he gestured for Rodney to unlock it.

The door slid open and John shot the minute he could see a figure. The guard went down, followed quickly by the one next to him as John fired again.

Kolya faced him, a gun pointed at John. John trained his P-90 on the commander and raised an eyebrow.

“Major,” Kolya said and there was a hint of surprise in his voice. “I see you have not yet succumbed to your hunger.”

“Not yet,” John said grimly. He knew he’d have a long road of recovery ahead of him, what with the fact he was pushing his body to the last of its meager energy reserves as he struggled to focus on the fight about to occur.

“Dr. McKay,” Kolya turned his eyes to Rodney.

John fired.

Kolya’s mouth dropped open slightly, surprise in his eyes as he stumbled backwards, clutching at the wounds in his chest. “I see,” he said, haltingly.

And then he fell to the ground.

It was almost anti-climactic, John thought as he stared down at the body of the man he’d been making a monster inside his own head for days.

“Don’t move,” Rodney said and John jerked. His mind was hazy from the lack of water and food, so much so that  _Rodney_ , who’d spent days being violated by the man John had just killed was more in control that John was.

Sora and Laden stood above Kolya’s body. Sora had a gun in hand, but she held it loosely.

“Drop the gun and surrender and I promise you will be given better treatment than we were,” John told them.

“Why?” Sora asked. “We starved you. The commander,” her eyes flicked to Rodney. “He hurt you in front of all of us. Why would you let us-”

“Because we’re better than that,” John said. “We’re not the enemies, Sora. We’re trying to destroy the Wraith, save this galaxy.”

“You invaded the city of the ancestors,” Laden stated. “This city isn’t yours to take.”

“Neither is it yours,” Rodney said. He was shivering around the edges and John took a deep breath.

“Atlantis is not just a city, she’s alive,” John told them. “She’s sentient, not just a possession that can change hands. She  _allowed_  us to settle on her and we will continue to do everything in our power to repay her, including destroying the creatures that threaten her.”

“The Wraith,” Sora stated.

“And any others,” John said, looking directly at her. “Drop your gun, Sora of the Genii.”

Sora’s hands shook and she nodded. “I haven’t agreed with this, not since,” she looked once again towards Rodney. “I apologize.”

“Don’t,” Rodney told her harshly. “You stood there and did nothing, you have no right to apologize.”

Sora dropped the gun and nodded. She held out her hands.

“You?” John asked Laden.

Laden frowned. “I… yes. Yes, I surrender.”

“Give me your gun,” John told Rodney. “And tie them up.”

Rodney did. Both Sora and Laden cooperated and soon enough they were tied at the wrists and weaponless.

“Come on,” John gestured with his gun and marched the two remaining Genii back to the room he and Rodney had been kept in.

Laden paled as soon as he saw it. “You promised-”

“I’m not going to starve you,” John told him. “Nor am I going to  _rape_  you. Right now, however, this is where you are going to stay while I get my people back on this city and we properly mourn our losses. Try to escape and I will kill you like I killed Kolya.”

Sora nodded smartly and pushed Laden into the room with her shoulder. “We understand, Major.”

John closed the door behind them and collapsed against the wall, breathing heavily. Now that the threat was over, he felt weak to the bone, but his work wasn’t done. Not yet.

“Rodney,” John said, clicking the radio.

“Yeah,” Rodney answered immediately. “Laden did a lot of damage to the systems trying to work the gate. I’m fixing what I can, but I’m going to need Grodin and Zelenka’s help.”

“We’ll get them,” John told him. “I’m going to the chair now.”

“I’ll meet you back here when you’re done,” Rodney said and the radio cut out.

John jogged to the transporter and then slowed to a walk as he neared the chair. He hoped he wouldn’t collapse in it.

He sat and leaned back at the chair turned under him. Atlantis’ response was immediate. Joy and relief mixed with worry for John and Rodney.

 _We’ll be fine_ , he told her.  _Can you open the gate back up?_

She did immediately and faded back into the city as John opened his eyes and staggered out of the chair.

The walk back to the gateroom was excruciating, but John got there. The first thing he noticed was Rodney, staring at Kolya’s body bleeding on the floor and he winced.

“Rodney,” he called, walking up to the man he loved. “Rodney, hey, you okay?”

Rodney seemed to wrench his eyes away from Kolya and onto John. He nodded. “Just relieved, I think. I don’t know, I don’t really feel… I feel numb.”

“It’s okay,” John told him. “That’s normal.”

“But you,” Rodney amended. “I feel my feelings for you. I didn’t return… I love you too, John. So much.”

John smiled and leaned forward to give Rodney a soft kiss. “I love you more than anything. Or anyone.”

Rodney smiled brightly. “Good.”

“Let’s bring our people home,” John said. “We need Carson to look at us, both of us, and we need to tell them about Elizabeth. It’s going to hit them hard…”

“We’ll get through it,” Rodney stated. “Our expedition is adaptable if nothing else.”

John hoped Rodney was talking about himself, he hoped he was. It relieved him, knowing that they could both heal from this.

“Dial the gate to Manara,” John told him.

Rodney nodded and did. The wormhole engaged and John clicked his radio. “Hello out there.”

“Major!” Ford answered. “We’re so glad you’re okay. We’ve been trying to contact Atlantis for days.”

“We hit a bit of snag,” John said. “The Genii tried to take over the city.”

“The Genii?” Teyla’s voice came on.

John let out a laugh, relief coursing through him like euphoria. “You guys have a lot to catch up on.”

“Yes, sir,” Ford said. “Should we start sending our people through?”

“Marines first, then civilians,” John ordered. “Meet you on the other side, Lieutenant.”

He clicked the radio off and turned to Rodney.

Rodney smiled at him and slipped his hand into John’s. John gave into his impulse and kissed the scientist once more on the lips before turning to greet the first of their men coming through the gate.


End file.
